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- EMDB-9674: Cryo-EM structure of CV-A10 mature virion -

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Basic information

Entry
Database: EMDB / ID: EMD-9674
TitleCryo-EM structure of CV-A10 mature virion
Map data
Sample
  • Virus: Coxsackievirus A10
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
  • Ligand: SPHINGOSINE
KeywordsCoxsackievirus A10 / Mature virion / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont genome entry into host cell via pore formation in plasma membrane / viral capsid / host cell cytoplasm / symbiont-mediated suppression of host gene expression / virion attachment to host cell / structural molecule activity
Similarity search - Function
Picornavirus coat protein / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesCoxsackievirus A10
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsChen JH / Ye XH
CitationJournal: Cell Discov / Year: 2019
Title: Coxsackievirus A10 atomic structure facilitating the discovery of a broad-spectrum inhibitor against human enteroviruses.
Authors: Jinhuan Chen / Xiaohua Ye / Xue-Yang Zhang / Zhengdan Zhu / Xiang Zhang / Zhijian Xu / Zhanyu Ding / Gang Zou / Qingwei Liu / Liangliang Kong / Wen Jiang / Weiliang Zhu / Yao Cong / Zhong Huang /
Abstract: Coxsackievirus A10 (CV-A10) belongs to the species A and is a causative agent of hand, foot, and mouth disease. Here we present cryo-EM structures of CV-A10 mature virion and native empty particle ...Coxsackievirus A10 (CV-A10) belongs to the species A and is a causative agent of hand, foot, and mouth disease. Here we present cryo-EM structures of CV-A10 mature virion and native empty particle (NEP) at 2.84 and 3.12 Å, respectively. Our CV-A10 mature virion structure reveals a density corresponding to a lipidic pocket factor of 18 carbon atoms in the hydrophobic pocket formed within viral protein 1. By structure-guided high-throughput drug screening and subsequent verification in cell-based infection-inhibition assays, we identified four compounds that inhibited CV-A10 infection in vitro. These compounds represent a new class of anti-enteroviral drug leads. Notably, one of the compounds, ICA135, also exerted broad-spectrum inhibitory effects on a number of representative viruses from all four species (A-D) of human enteroviruses. Our findings should facilitate the development of broadly effective drugs and vaccines for enterovirus infections.
History
DepositionOct 6, 2018-
Header (metadata) releaseNov 7, 2018-
Map releaseNov 7, 2018-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6iij
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6iij
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9674.png

Downloads & links

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Map

FileDownload / File: emd_9674.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 432 pix.
= 434.16 Å		1.01 Å/pix.
x 432 pix.
= 434.16 Å		1.01 Å/pix.
x 432 pix.
= 434.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.005 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.6 / Movie #1: 1.6
Minimum - Maximum-9.277205 - 15.515470000000001
Average (Standard dev.)-0.000000000384173 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 434.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0051.0051.005
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z434.160434.160434.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-9.27715.515-0.000

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Supplemental data

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Sample components

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Entire : Coxsackievirus A10

EntireName: Coxsackievirus A10
Components
  • Virus: Coxsackievirus A10
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
  • Ligand: SPHINGOSINE

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Supramolecule #1: Coxsackievirus A10

SupramoleculeName: Coxsackievirus A10 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 42769 / Sci species name: Coxsackievirus A10 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A10
Molecular weightTheoretical: 33.088219 KDa
SequenceString: GDPVEDIIHD ALGNTARRAI SGATNVESAA DTTPSSHRLE TGRVPALQAA ETGATSNATD ENMIETRCVI NRNGVLETTI NHFFSRSGL VGVVNLTDGG DTTGYATWDI DIMGFVQLRR KCEMFTYMRF NAEFTFVTTT KSGEARPYML QYMYVPPGAP K PTGRDAFQ ...String:
GDPVEDIIHD ALGNTARRAI SGATNVESAA DTTPSSHRLE TGRVPALQAA ETGATSNATD ENMIETRCVI NRNGVLETTI NHFFSRSGL VGVVNLTDGG DTTGYATWDI DIMGFVQLRR KCEMFTYMRF NAEFTFVTTT KSGEARPYML QYMYVPPGAP K PTGRDAFQ WQTATNPSVF VKLTDPPAQV SVPFMSPASA YQWFYDGYPT FGQHPETSNT TYGLCPNNMM GTFAVRVVSR EA SQLKLQT RVYMKLKHVR AWVPRPIRSQ PYLLKNFPNY DSSKITNSAR DRSSIKQANM

UniProtKB: Genome polyprotein

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A10
Molecular weightTheoretical: 27.741023 KDa
SequenceString: SPSVEACGYS DRVAQLTVGN SSITTQEAAN IVLAYGEWPE YCPDTDATAV DKPTRPDVSV NRFYTLDSKM WQENSTGWYW KFPDVLNKT GVFGQNAQFH YLYRSGFCLH VQCNASKFHQ GALLVAVIPE FVIAGRGSNT KPNEAPHPGF TTTFPGTTGA T FHDPYVLD ...String:
SPSVEACGYS DRVAQLTVGN SSITTQEAAN IVLAYGEWPE YCPDTDATAV DKPTRPDVSV NRFYTLDSKM WQENSTGWYW KFPDVLNKT GVFGQNAQFH YLYRSGFCLH VQCNASKFHQ GALLVAVIPE FVIAGRGSNT KPNEAPHPGF TTTFPGTTGA T FHDPYVLD SGVPLSQALI YPHQWVNLRT NNCATVIVPY INAVPFDSAI NHSNFGLVVV PVSPLKYSSG ATTAIPITIT IA PLNSEFG GLRQAVSQ

UniProtKB: Genome polyprotein

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A10
Molecular weightTheoretical: 26.187623 KDa
SequenceString: GIPAELRPGT NQFLTTDDDT AAPILPGFTP TPTIHIPGEV HSLLELCRVE TILEVNNTTE ATGLTRLLIP VSSQNKADEL CAAFMVDPG RIGPWQSTLV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LVAYSPPGSA QPANRETAML GTHVIWDFGL Q SSVSLVIP ...String:
GIPAELRPGT NQFLTTDDDT AAPILPGFTP TPTIHIPGEV HSLLELCRVE TILEVNNTTE ATGLTRLLIP VSSQNKADEL CAAFMVDPG RIGPWQSTLV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LVAYSPPGSA QPANRETAML GTHVIWDFGL Q SSVSLVIP WISNTHFRTA KTGGNYDYYT AGVVTLWYQT NYVVPPETPG EAYIIAMGAA QDNFTLKICK DTDEVTQQAV LQ

UniProtKB: Genome polyprotein

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Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A10
Molecular weightTheoretical: 7.464104 KDa
SequenceString:
MGAQVSTQKS GSHETGNVAT GGSTINFTNI NYYKDSYAAS ATRQDFTQDP KKFTQPVLDS IRELSAPLN

UniProtKB: Genome polyprotein

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Macromolecule #5: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13273
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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